Is EXPH5 p.Lys891Asn (c.2673G>T) pathogenic?

EXPH5 p.Lys891Asn (c.2673G>T) is classified Likely benign in EXPH5 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-22). AlphaMissense: likely benign (0.0709); Ultra-rare (popmax 0.024%, afr); Associated with Inborn genetic diseases.

What condition is associated with EXPH5 p.Lys891Asn (c.2673G>T)?

EXPH5 p.Lys891Asn (c.2673G>T) is associated with Inborn genetic diseases (ClinVar).

How common is EXPH5 p.Lys891Asn (c.2673G>T) in the general population?

EXPH5 p.Lys891Asn (c.2673G>T) is ultra-rare (popmax 0.024%, afr) (gnomAD).

What do computational predictors say about EXPH5 p.Lys891Asn (c.2673G>T)?

AlphaMissense predicts likely benign (score 0.0709) — an in-silico prediction, not a clinical call.

EXPH5 p.Lys891Asn

c.2673G>T · VCV3276853

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0709 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.024%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0709	likely benign
REVEL	0.049	moderately benign-leaning
SaProt	LLR -6.57	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 0.066	GERP -0.61
Regional constraint	o/e 0.99	unconstrained · MANE · 84 kb · p 0.73 · regional, not allelic
Overall
CADD	0.34	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

Grpmax group 0.024% African / African-American · 18/75,052 alleles

Filtering AF 0.0154% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0128%

Overall 0.0013% 21/1,614,162 alleles · ultra-rare exomes 15/1,461,858 · genomes 6/152,304 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.024%	4,170
Remaining individualsnot grpmax-eligible	0.0032%	31,255
Admixed American	0.00167%	60,020

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: EXPH5
Protein: p.Lys891Asn
Coding: c.2673G>T
MANE Select: NM_015065
Type: single nucleotide variant
Location: chr11:108512834 (GRCh38)
Gene constraint: LOEUF 1.142 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 36.39
Residue 891: the 'disordered' region

Full EXPH5 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

EXPH5 p.Ala1429Ser Uncertain significance ★★ ⚠ same condition
EXPH5 p.Arg1727Lys Uncertain significance ★★ ⚠ same condition
EXPH5 p.Asn1548Asp Uncertain significance ★★ ⚠ same condition
EXPH5 p.Asp741His Uncertain significance ★★ ⚠ same condition
EXPH5 p.Gln1464Arg Uncertain significance ★★ ⚠ same condition
EXPH5 p.Gly54Arg Uncertain significance ★★ ⚠ same condition
EXPH5 p.Leu1519Arg Uncertain significance ★★ ⚠ same condition
EXPH5 p.Leu234Phe 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/exph5-p-lys891asn (accessed [today's date]).

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