Is KRT14 p.Ser55Pro (c.163T>C) pathogenic?

KRT14 p.Ser55Pro (c.163T>C) is classified Uncertain significance in KRT14 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-11). AlphaMissense: likely benign (0.2479); Absent from gnomAD v4.1.

How common is KRT14 p.Ser55Pro (c.163T>C) in the general population?

KRT14 p.Ser55Pro (c.163T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about KRT14 p.Ser55Pro (c.163T>C)?

AlphaMissense predicts likely benign (score 0.2479) — an in-silico prediction, not a clinical call.

KRT14 p.Ser55Pro

c.163T>C · rs2144586557 · VCV1499780

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2479 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.2479	likely benign
REVEL	0.365	indeterminate
SaProt	LLR -10.62	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.63	GERP 1.7, phastCons 0.05
Regional constraint	o/e 0.84	unconstrained · MANE · 4,396 bp · p 3e-05 · regional, not allelic
Overall
CADD	17.3	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: KRT14
Protein: p.Ser55Pro
Coding: c.163T>C
MANE Select: NM_000526
dbSNP: rs2144586557
Type: single nucleotide variant
Location: chr17:41586672 (GRCh38)
Gene constraint: LOEUF 0.932 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.00 · 6 PDB
Residue 55: the 'head' region

Full KRT14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

KRT14 c.526-2A>C Likely pathogenic ★★ same type
KRT14 c.927+1G>A Pathogenic ★★ same type
KRT14 p.Arg125Cys Pathogenic ★★ same type
KRT14 p.Arg125His Pathogenic ★★ same type
KRT14 p.Arg125Leu Pathogenic ★★ same type
KRT14 p.Arg288Leu Pathogenic/Likely pathogenic ★★ same type
KRT14 p.Arg388Cys Pathogenic/Likely pathogenic ★★ same type
KRT14 p.Arg388His Likely pathogenic ★★ 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/krt14-p-ser55pro (accessed [today's date]).

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