Is SNIP1 p.Gly26Val (c.77G>T) pathogenic?

SNIP1 p.Gly26Val (c.77G>T) is classified Uncertain significance in SNIP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-06). AlphaMissense: likely benign (0.0986); Very rare (popmax 0.00856%, nfe).

How common is SNIP1 p.Gly26Val (c.77G>T) in the general population?

SNIP1 p.Gly26Val (c.77G>T) is very rare (popmax 0.00856%, nfe) (gnomAD).

What do computational predictors say about SNIP1 p.Gly26Val (c.77G>T)?

AlphaMissense predicts likely benign (score 0.0986) — an in-silico prediction, not a clinical call.

SNIP1 p.Gly26Val

c.77G>T · VCV3799492

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0986 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00856%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0986	likely benign
REVEL	0.012	strongly benign-leaning
SaProt	LLR -6.93	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 2.9	GERP -2, phastCons 0.63
Regional constraint	o/e 0.85	unconstrained · MANE · 16 kb · p 0.00046 · regional, not allelic
Overall
CADD	11.02	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 0.00856% European (non-Finnish) · 101/1,179,412 alleles

Filtering AF 0.00716% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00668%

Overall 0.00657% 106/1,612,686 alleles · very rare exomes 102/1,460,472 · genomes 4/152,214 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00856%	11,677
Remaining individualsnot grpmax-eligible	0.00481%	20,809
African / African-American	0.00267%	37,463

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: SNIP1
Protein: p.Gly26Val
Coding: c.77G>T
MANE Select: NM_024700
Type: single nucleotide variant
Location: chr1:37554153 (GRCh38)
Gene constraint: LOEUF 0.865 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.66 · 10 PDB
Residue 26: the 'disordered' region

Full SNIP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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SNIP1 p.Asp383Gly Uncertain significance ★★ ⚠ same type
SNIP1 p.Asp386Asn Uncertain significance ★★ ⚠ same type
SNIP1 p.Asp386Glu Uncertain significance ★★ ⚠ same type
SNIP1 p.Glu32Ala Uncertain significance ★★ ⚠ same type
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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/snip1-p-gly26val (accessed [today's date]).

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