Variant classification summary

NM_020975.6:c.2410G>T

RET · NP_066124.1:p.(Val804Leu) · NM_020975.6

GRCh37: chr10:43614996 G>T · GRCh38: chr10:43119548 G>T

Gene: RET Transcript: NM_020975.6

Final call

Likely Pathogenic

PS3 supporting PM1 moderate PM2 supporting PM5 supporting PP1 supporting

Variant details

Gene

RET

Transcript

NM_020975.6

Protein

NP_066124.1:p.(Val804Leu)

gnomAD AF

1.3080004783544607e-05 (v4.1)

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_020975.6:c.2410G>T (p.Val804Leu) in RET is classified as Likely Pathogenic using generic ACMG/AMP 2015 framework (Richards et al., PMID:25741868).

2

PM1 (moderate): Val804 is in the RET tyrosine kinase domain, a critical functional domain where MEN2/FMTC-associated missense mutations cluster. Multiple publications identify codon 804 as a disease-associated residue.

3

PS3 (supporting): Functional studies directly characterized RET V804L among seven kinase domain mutations; the variant was introduced and biologically assessed (Iwashita et al., 1999).

4

PM2 (supporting): Extremely low allele frequency in population databases. gnomAD v2.1 AF=4.3×10⁻⁶ (1/232,600); gnomAD v4.1 AF=1.3×10⁻⁵ (21/1,605,504); absent from gnomAD-Canada.

5

PM5 (supporting): V804M (c.2410G>A) is a well-established pathogenic variant at the same residue, reported as FMTC-causing in PMID:10876191. Per ACMG/AMP PM5, a novel missense at a residue with a known pathogenic missense change provides supporting evidence.

6

PP1 (supporting): Co-segregation of V804L with familial medullary thyroid cancer in an extended kindred is reported in PMID:12694233.

7

Overall: 1 moderate (PM1) + 4 supporting (PS3, PM2, PM5, PP1) criteria met. This satisfies the '1 Moderate and 4 Supporting' Likely Pathogenic combination under generic ACMG/AMP 2015 rules.

8

No benign criteria were met. BA1 (AF>1%): not met. BS1 (AF>0.3%): not met. BS3 (functional evidence of no damage): not met — available functional evidence supports damaging effect.

9

ClinVar consensus supports pathogenicity: 18 clinical laboratories classify as Pathogenic (ClinVar Variation ID: 13946), though most submissions are single-submitter review status without expert panel review.

10

Several criteria require human review: PS3 strength may be upgradable with full-text review of PMID:10445857 and PMID:15184865; PP1 strength may be upgradable with full-text segregation data; PM1 should be confirmed against germline-specific hotspot methodology.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Pathogenic classification based on the observed combination of pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_020975.6:c.2410G>T (p.Val804Leu) is a missense substitution. PVS1 is reserved for null variants (nonsense, frameshift, canonical ±1,2 splice sites). The variant does not fall into any PVS1 bucket per ClinGen SVI PVS1 framework (PMC6185798).
PS1	Not assessed	No evidence of a different nucleotide change at the same position (c.2410) with independently established pathogenicity was identified.
PS2	Not assessed	No de novo report for NM_020975.6:c.2410G>T was identified in the literature reviewed. PM6/PS2 require a confirmed de novo observation with maternity and paternity confirmation.
PS3	Met	Functional characterization of V804L was performed in PMID:10445857 (Iwashita et al., 1999). The study introduced seven RET kinase domain mutations including V804L and assessed their biological and biochemical properties. The abstract confirms V804L was directly studied. This provides variant-specific functional evidence supporting a deleterious effect, consistent with the known gain-of-function mechanism of RET kinase domain mutations in MEN2/FMTC.	PMID:10445857
PS4	Not assessed	Insufficient statistical case-control data to meet PS4 threshold. While this variant is reported by 18 clinical laboratories in ClinVar as Pathogenic and appears in multiple clinical/familial contexts, specific proband counts, case-control statistics, and odds ratios are not available in the evidence sources reviewed. PS4 requires PM2 first (met) plus statistically significant enrichment in affected individuals versus controls.	clinvar
PS5	N/A	Independent evaluation of available evidence is being performed, making PS5 (reputable source reports as pathogenic without available evidence) not applicable.
PM1	Met	Val804 is located in the RET tyrosine kinase domain (codons 724–1010), a critical and well-established functional domain. Multiple independent publications identify codon 804 as a disease-associated residue in MEN2 and FMTC (PMID:15184865, PMID:9242375, PMID:10445857, PMID:10235148, PMID:12694233). The automated hotspot analysis flagged this residue as not statistically significant in somatic cancer, but this does not diminish the established role of RET kinase domain residues in germline MEN2/FMTC predisposition. No benign missense variation is observed at this specific residue in gnomAD.	PMID:15184865 PMID:9242375 PMID:10445857 PMID:12694233
PM2	Met	The variant is extremely rare in population databases. gnomAD v2.1: 1/232,600 alleles (AF=4.3×10⁻⁶). gnomAD v4.1: 21/1,605,504 alleles (AF=1.3×10⁻⁵; grpmax FAF=8.04×10⁻⁶). Both are well below the 0.1% PM2 threshold for non-VCEP frameworks. Absent from gnomAD-Canada v1.0. No homozygotes observed.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Met	NM_020975.6:c.2410G>A (p.Val804Met, V804M) is a well-established pathogenic variant at the same amino acid residue. PMID:10876191 (Feldman et al., 2000) reports a family with FMTC due to the RET V804M mutation. V804M is classified as Pathogenic in ClinVar. Per ACMG/AMP PM5, a novel missense change at an amino acid residue where a different missense change has been determined to be pathogenic can be applied as supporting evidence.	PMID:10876191
PM6	Not assessed	No de novo observation for NM_020975.6:c.2410G>T with confirmed maternity and paternity was identified in the reviewed literature.
PP1	Met	Co-segregation of the V804L mutation with familial medullary thyroid cancer (FMTC) was demonstrated in an extended kindred as reported in PMID:12694233. The title and abstract confirm 'Segregation of the V804L mutation... in an extended kindred with familial medullary thyroid cancer.' This provides evidence of co-segregation with disease in a gene definitively known to cause MEN2/FMTC.	PMID:12694233
PP2	Not met	While RET missense variants are a well-established mechanism of disease in MEN2/FMTC (gain-of-function), PP2 also requires a low rate of benign missense variation in the gene. RET has observable benign missense variation in population databases (gnomAD), and the gene's missense Z-score is not sufficiently extreme to meet the low benign missense rate requirement of PP2.	gnomad_v2 gnomad_v4
PP3	Not met	In silico evidence is mixed and does not meet the threshold for multiple lines of computational support for a deleterious effect. REVEL score 0.715 leans pathogenic but is below the strong pathogenic range (≥0.9). BayesDel score 0.338 does not support pathogenicity (leans benign). SpliceAI max delta 0.01 predicts no splicing impact. Only one of three computational tools supports a deleterious effect.	revel bayesdel spliceai
PP4	Not assessed	Insufficient patient-specific phenotype data available in the evidence sources to determine whether the patient's phenotype or family history is highly specific for MEN2/FMTC with a single genetic etiology.
PP5	N/A	Independent evaluation of available evidence is being performed. ClinVar reports this variant as Pathogenic by 18 clinical laboratories, but the evidence is accessible for independent assessment. PP5 is reserved for situations where reputable sources report the variant as pathogenic but the evidence is not available for independent evaluation.
BA1	Not met	The variant has an allele frequency of ~4.3×10⁻⁶ in gnomAD v2.1 and 1.3×10⁻⁵ in gnomAD v4.1, far below the 1% BA1 threshold.	gnomad_v2 gnomad_v4
BS1	Not met	Maximum subpopulation allele frequency is 5.2×10⁻⁵ in European (Finnish) in gnomAD v2.1 and 1.0×10⁻⁴ in Ashkenazi Jewish in gnomAD v4.1, both well below the 0.3% BS1 threshold.	gnomad_v2 gnomad_v4
BS2	Not met	RET-MEN2/FMTC is an autosomal dominant disorder with high penetrance. Only 1 allele was observed in gnomAD v2.1 and 21 in v4.1. A single observation cannot establish that the variant is observed in healthy adults without disease, especially given the late-onset and variable expressivity of MEN2/FMTC.	gnomad_v2 gnomad_v4
BS3	Not met	Available functional evidence supports a damaging effect, not a benign effect. PMID:10445857 studied V804L among kinase domain mutations and the variant is consistently associated with MEN2/FMTC in clinical and functional literature. BS3 requires well-established functional studies showing no damaging effect.	PMID:10445857
BS4	Not met	Available segregation evidence supports co-segregation with disease, not lack of segregation. PMID:12694233 reports segregation of V804L with FMTC in an extended kindred. BS4 requires lack of co-segregation in affected family members.	PMID:12694233
BP1	Not met	RET disease mechanism in MEN2/FMTC is primarily gain-of-function missense variants, not truncating variants. BP1 applies when a gene's disease mechanism is primarily through truncating variants and the observed variant is missense. The opposite is true for RET — missense variants are the established pathogenic mechanism.
BP2	Not assessed	No phase information is available to determine whether this variant has been observed in trans with a pathogenic RET variant (relevant for fully penetrant dominant disorders) or in cis with a pathogenic variant in any inheritance pattern.
BP4	Not met	Multiple lines of computational evidence do not consistently support a benign effect. REVEL 0.715 predicts a deleterious effect. BayesDel 0.338 does not strongly indicate benign. SpliceAI shows no splice impact. The in silico evidence is mixed and does not meet the BP4 threshold requiring multiple lines of computational evidence supporting no impact.	revel bayesdel spliceai
BP5	Not assessed	No evidence that this variant was observed in a case with a definitive alternate molecular basis for disease was identified in the reviewed materials.
BP6	Not met	ClinVar reports this variant as Pathogenic by 18 clinical laboratories. No reputable source reports it as benign. BP6 requires a reputable source to report the variant as benign with inaccessible evidence.	clinvar
BP7	N/A	NM_020975.6:c.2410G>T (p.Val804Leu) is a missense variant, not synonymous. BP7 applies only to synonymous (silent) variants with no predicted splice impact and low nucleotide conservation.

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