Is CDIP1 p.Pro51Ser (c.151C>T) pathogenic?

CDIP1 p.Pro51Ser (c.151C>T) is classified Uncertain significance in CDIP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-06). AlphaMissense: likely benign (0.2756); Very rare (popmax 0.00936%, afr).

How common is CDIP1 p.Pro51Ser (c.151C>T) in the general population?

CDIP1 p.Pro51Ser (c.151C>T) is very rare (popmax 0.00936%, afr) (gnomAD).

What do computational predictors say about CDIP1 p.Pro51Ser (c.151C>T)?

AlphaMissense predicts likely benign (score 0.2756) — an in-silico prediction, not a clinical call.

CDIP1 p.Pro51Ser

c.151C>T · VCV3489127

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2756 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00936%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2756	likely benign
REVEL	0.376	indeterminate
SaProt	LLR -10.82	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 1,555 bp · p 0.37 · regional, not allelic
Overall
CADD	26.2	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 0.00936% African / African-American · 7/74,762 alleles

Filtering AF 0.00438% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00309%

Overall 0.00056% 9/1,605,874 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00936%	10,680
Remaining individualsnot grpmax-eligible	0.00161%	62,150
European (non-Finnish)	8.52e-05%	1,174,133

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: CDIP1
Protein: p.Pro51Ser
Coding: c.151C>T
MANE Select: NM_013399
Type: single nucleotide variant
Location: chr16:4513786 (GRCh38)
Gene constraint: LOEUF 1.142 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 55.37
Residue 51: the 'disordered' region

Full CDIP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDIP1 p.Ala122Thr Uncertain significance ★ ⚠ same type
CDIP1 p.Ala136Ser Uncertain significance ★ ⚠ same type
CDIP1 p.Ala34Gly Uncertain significance ★ ⚠ same type
CDIP1 p.Arg30His Uncertain significance ★ ⚠ same type
CDIP1 p.Asp48Asn Uncertain significance ★ ⚠ same type
CDIP1 p.Asp74His Uncertain significance ★ ⚠ same type
CDIP1 p.Gln37Leu Uncertain significance ★ ⚠ same type
CDIP1 p.Gly172Arg 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/cdip1-p-pro51ser (accessed [today's date]).

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