Is CEMIP p.Pro278Ser (c.832C>T) pathogenic?

CEMIP p.Pro278Ser (c.832C>T) is classified Likely benign in CEMIP (ClinVar, Single submitter, 1 submitter; last evaluated 2019-05-16). AlphaMissense: likely benign (0.1052); Rare (popmax 0.209%, nfe).

How common is CEMIP p.Pro278Ser (c.832C>T) in the general population?

CEMIP p.Pro278Ser (c.832C>T) is rare (popmax 0.209%, nfe) (gnomAD).

What do computational predictors say about CEMIP p.Pro278Ser (c.832C>T)?

AlphaMissense predicts likely benign (score 0.1052) — an in-silico prediction, not a clinical call.

CEMIP p.Pro278Ser

c.832C>T · rs138423783 · VCV804688

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1052 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.209%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1052	likely benign
REVEL	0.231	benign-leaning
SaProt	LLR -8.47	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 7.4	GERP 2.5, phastCons 1
Regional constraint	o/e 0.39	unconstrained · MANE · 1,044 bp · p 5.3e-05 · regional, not allelic
Overall
CADD	19.48	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 0.209% European (non-Finnish) · 2,461/1,179,816 alleles

Filtering AF 0.202% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.199%

Overall 0.17% 2,743/1,613,294 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.209%	479
Remaining individualsnot grpmax-eligible	0.144%	694
Admixed American	0.0883%	1,132
South Asian	0.0791%	1,265
African / African-American	0.052%	1,923
Finnishnot grpmax-eligible	0.0378%	2,643
Middle Eastern	0.033%	3,030
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,596
East Asian	0.00223%	44,878

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: CEMIP
Protein: p.Pro278Ser
Coding: c.832C>T
MANE Select: NM_001293298
dbSNP: rs138423783
Type: single nucleotide variant
Location: chr15:80887728 (GRCh38)
Gene constraint: LOEUF 0.764 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.69
Residue 278: the gg-type lectin 1 domain

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

Similar variants

CEMIP p.Ala33Val Uncertain significance ★★ ⚠ same type
CEMIP p.Gly870Asp Uncertain significance ★★ ⚠ same type
CEMIP c.1086+82T>A Benign ★★ same type
CEMIP c.1087-239G>A Benign ★★ same type
CEMIP c.1412-76G>A Benign ★★ same type
CEMIP c.1587+57A>G Benign ★★ same type
CEMIP c.1587+79G>A Benign ★★ same type
CEMIP c.1797+102T>C 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/cemip-p-pro278ser (accessed [today's date]).

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