Is ST14 p.Ser24Phe (c.71C>T) pathogenic?

ST14 p.Ser24Phe (c.71C>T) is classified Uncertain significance in ST14 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-17). AlphaMissense: likely benign (0.1368); Very rare (popmax 9.2e-05%, nfe); Associated with Inborn genetic diseases.

What condition is associated with ST14 p.Ser24Phe (c.71C>T)?

ST14 p.Ser24Phe (c.71C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ST14 p.Ser24Phe (c.71C>T) in the general population?

ST14 p.Ser24Phe (c.71C>T) is very rare (popmax 9.2e-05%, nfe) (gnomAD).

What do computational predictors say about ST14 p.Ser24Phe (c.71C>T)?

AlphaMissense predicts likely benign (score 0.1368) — an in-silico prediction, not a clinical call.

ST14 p.Ser24Phe

c.71C>T · rs2540734835 · VCV3170602

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1368 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 9.2e-05%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1368	likely benign
REVEL	0.346	indeterminate
SaProt	LLR -7.25	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.5	GERP 0.4, phastCons 0.99
Regional constraint	o/e 0.90	unconstrained · MANE · 50 kb · p 0.00036 · regional, not allelic
Overall
CADD	24.6	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 9.2e-05% European (non-Finnish) · 1/1,086,926 alleles

Overall 6.96e-05% 1/1,436,064 alleles · very rare exomes 1/1,284,318 · genomes 0/151,746 · 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: ST14
Protein: p.Ser24Phe
Coding: c.71C>T
MANE Select: NM_021978
dbSNP: rs2540734835
Type: single nucleotide variant
Location: chr11:130160050 (GRCh38)
Gene constraint: LOEUF 0.589 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 81.23 · 25 PDB

Full ST14 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

ST14 p.Ala557Thr Uncertain significance ★★ ⚠ same condition
ST14 p.Arg227Gly Uncertain significance ★★ ⚠ same condition
ST14 p.Gly272Ser Uncertain significance ★★ ⚠ same condition
ST14 p.Gly642Ser Uncertain significance ★★ ⚠ same condition
ST14 p.Lys743Asn Uncertain significance ★★ ⚠ same condition
ST14 p.Pro526Leu Uncertain significance ★★ ⚠ same condition
ST14 p.Ser449Phe Uncertain significance ★★ ⚠ same condition
ST14 p.Thr419Ala 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/st14-p-ser24phe (accessed [today's date]).

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