Is SELE p.Ser61Phe (c.182C>T) pathogenic?

SELE p.Ser61Phe (c.182C>T) is classified Uncertain significance in SELE (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-29). AlphaMissense: likely benign (0.1725); Absent from gnomAD v4.1.

How common is SELE p.Ser61Phe (c.182C>T) in the general population?

SELE p.Ser61Phe (c.182C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SELE p.Ser61Phe (c.182C>T)?

AlphaMissense predicts likely benign (score 0.1725) — an in-silico prediction, not a clinical call.

SELE p.Ser61Phe

c.182C>T · VCV4582048

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1725 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1725	likely benign
REVEL	0.086	moderately benign-leaning
SaProt	LLR -12.32	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.4	GERP -0.24, phastCons 0.21
Regional constraint	o/e 1.03	unconstrained · MANE · 7,865 bp · p 0.43 · regional, not allelic
Overall
CADD	22.3	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SELE
Protein: p.Ser61Phe
Coding: c.182C>T
MANE Select: NM_000450
Type: single nucleotide variant
Location: chr1:169732854 (GRCh38)
Gene constraint: LOEUF 0.86 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.28 · 17 PDB
Residue 61: a disulfide bond; the c-type lectin domain; an α-helix

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

Similar variants

SELE p.Glu277Lys Uncertain significance ★★ ⚠ same type
SELE p.Phe325Leu Uncertain significance ★★ ⚠ same type
SELE p.Asn291= Benign ★★ same type
SELE p.Asn420= Benign ★★ same type
SELE p.Glu295Lys Benign ★★ same type
SELE p.Glu421Gln Benign ★★ same type
SELE p.Leu575Phe Benign ★★ same type
SELE c.901+9G>T 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/sele-p-ser61phe (accessed [today's date]).

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