Is SIN3B p.Ser31Phe (c.92C>T) pathogenic?

SIN3B p.Ser31Phe (c.92C>T) is classified Uncertain significance in SIN3B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-06). AlphaMissense: likely benign (0.1657); Very rare (popmax 0.000203%, nfe).

How common is SIN3B p.Ser31Phe (c.92C>T) in the general population?

SIN3B p.Ser31Phe (c.92C>T) is very rare (popmax 0.000203%, nfe) (gnomAD).

What do computational predictors say about SIN3B p.Ser31Phe (c.92C>T)?

AlphaMissense predicts likely benign (score 0.1657) — an in-silico prediction, not a clinical call.

SIN3B p.Ser31Phe

c.92C>T · rs1971249953 · VCV2752222

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1657 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000203%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1657	likely benign
REVEL	0.052	moderately benign-leaning
SaProt	LLR -9.72	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 5.2	GERP 0.15, phastCons 0.97
Regional constraint	o/e 0.75	unconstrained · MANE · 33 kb · p 7e-09 · regional, not allelic
Overall
CADD	23.2	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 0.000203% European (non-Finnish) · 2/983,816 alleles

Filtering AF 3.4e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.3e-05%

Overall 0.000163% 2/1,225,914 alleles · very rare exomes 2/1,073,958 · genomes 0/151,956 · joint denominator

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: SIN3B
Protein: p.Ser31Phe
Coding: c.92C>T
MANE Select: NM_001297595
dbSNP: rs1971249953
Type: single nucleotide variant
Location: chr19:16829512 (GRCh38)
Gene constraint: LOEUF 0.245 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.07 · 4 PDB
Residue 31: the 'interaction with cry1' region

Full SIN3B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SIN3B p.Ala534Thr Uncertain significance ★★ same type
SIN3B p.Glu258Asp Uncertain significance ★★ ⚠ same type
SIN3B p.His91Tyr Uncertain significance ★★ ⚠ same type
SIN3B p.Pro281Ala Uncertain significance ★★ ⚠ same type
SIN3B p.Val160Met Uncertain significance ★★ ⚠ same type
SIN3B p.Val873Ile Uncertain significance ★★ ⚠ same type
SIN3B c.1266+354G>A Benign ★★ same type
SIN3B c.2954+6A>G Benign ★★ 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/sin3b-p-ser31phe (accessed [today's date]).

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