Is MYC p.Ser362Phe (c.1085C>T) pathogenic?

MYC p.Ser362Phe (c.1085C>T) is classified Benign/Likely benign in MYC (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-08-18). AlphaMissense: ambiguous (0.4142); Low-frequency (popmax 1.03%, sas).

How common is MYC p.Ser362Phe (c.1085C>T) in the general population?

MYC p.Ser362Phe (c.1085C>T) is low-frequency (popmax 1.03%, sas) (gnomAD).

What do computational predictors say about MYC p.Ser362Phe (c.1085C>T)?

AlphaMissense predicts ambiguous (score 0.4142) — an in-silico prediction, not a clinical call.

MYC p.Ser362Phe

c.1085C>T · rs200431478 · VCV719682

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

ambiguous

0.4142 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.03%, sas)

Computational evidence

Protein change
AlphaMissense	0.4142	ambiguous
REVEL	0.445	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.3, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 2,237 bp · p 0.38 · regional, not allelic
Overall
CADD	27.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM S347F vs ClinVar S362F) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.03% South Asian · 940/91,072 alleles

Filtering AF 0.977% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.955%

Overall 0.0991% 1,599/1,614,078 alleles · low-frequency

Ancestry group	Frequency	1 in
South Asiangrpmax	1.03%	97
Middle Eastern	0.858%	117
Remaining individualsnot grpmax-eligible	0.125%	801
Admixed American	0.0667%	1,500
European (non-Finnish)	0.0411%	2,433
African / African-American	0.00533%	18,749

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MYC
Protein: p.Ser362Phe
Coding: c.1085C>T
MANE Select: NM_002467
dbSNP: rs200431478
Type: single nucleotide variant
Location: chr8:127740678 (GRCh38)
Gene constraint: LOEUF 0.128 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 61.38 · 25 PDB
Residue 362: a modified residue (phosphoserine)

Full MYC gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MYC p.Asn26Ser Uncertain significance ★★ ⚠ same type
MYC p.Gln48= Benign ★★ same type
MYC p.Phe22Leu Benign/Likely benign ★★ same type
MYC p.Thr73Ala Pathogenic ★ same type
MYC c.30+4A>T Uncertain significance ★ same type
MYC p.Ala224Val Uncertain significance ★ ⚠ same type
MYC p.Ala230Ser Uncertain significance ★ ⚠ same type
MYC p.Asp433His Uncertain significance ★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/myc-p-ser362phe (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown