Is SIM1 p.Met513Ile (c.1539G>T) pathogenic?

SIM1 p.Met513Ile (c.1539G>T) is classified Uncertain significance in SIM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-16). AlphaMissense: likely benign (0.3167); Ultra-rare (popmax 0.034%, mid); Associated with Inborn genetic diseases.

What condition is associated with SIM1 p.Met513Ile (c.1539G>T)?

SIM1 p.Met513Ile (c.1539G>T) is associated with Inborn genetic diseases (ClinVar).

How common is SIM1 p.Met513Ile (c.1539G>T) in the general population?

SIM1 p.Met513Ile (c.1539G>T) is ultra-rare (popmax 0.034%, mid) (gnomAD).

What do computational predictors say about SIM1 p.Met513Ile (c.1539G>T)?

AlphaMissense predicts likely benign (score 0.3167) — an in-silico prediction, not a clinical call.

SIM1 p.Met513Ile

c.1539G>T · rs1186169091 · VCV2250343

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3167 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.034%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3167	likely benign
REVEL	0.158	moderately benign-leaning
SaProt	LLR -5.55	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.5	GERP 2.1, phastCons 1
Regional constraint	o/e 1.07	unconstrained · MANE · 31 kb · p 0.14 · regional, not allelic
Overall
CADD	21.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.034% Middle Eastern · 2/5,876 alleles

Filtering AF 0.00599% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00248%

Overall 0.000637% 10/1,570,602 alleles · ultra-rare exomes 9/1,418,396 · genomes 1/152,206 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.034%	2,938
South Asian	0.00467%	21,434
European (non-Finnish)	0.000346%	288,805

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: SIM1
Protein: p.Met513Ile
Coding: c.1539G>T
MANE Select: NM_005068
dbSNP: rs1186169091
Type: single nucleotide variant
Location: chr6:100393518 (GRCh38)
Gene constraint: LOEUF 0.332 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 60.70
Residue 513: the single-minded c-terminal domain

Full SIM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SIM1 p.Cys434Ter Pathogenic ★★ same condition
SIM1 p.Ala495Gly Uncertain significance ★★ ⚠ same condition
SIM1 p.Arg548Gln Uncertain significance ★★ ⚠ same condition
SIM1 p.Cys605Tyr Uncertain significance ★★ ⚠ same condition
SIM1 p.Glu552Lys Uncertain significance ★★ ⚠ same condition
SIM1 p.Glu617Lys Uncertain significance ★★ ⚠ same condition
SIM1 p.Glu725Lys Uncertain significance ★★ same condition
SIM1 p.Gly203Cys Uncertain significance ★★ ⚠ same condition

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/sim1-p-met513ile (accessed [today's date]).

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