Is TRAF7 p.Ser624= (c.1872C>T) pathogenic?

TRAF7 p.Ser624= (c.1872C>T) is classified Likely benign in TRAF7 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-01-31). Rare (popmax 0.216%, afr); Associated with TRAF7-related disorder.

What condition is associated with TRAF7 p.Ser624= (c.1872C>T)?

TRAF7 p.Ser624= (c.1872C>T) is associated with TRAF7-related disorder (ClinVar).

How common is TRAF7 p.Ser624= (c.1872C>T) in the general population?

TRAF7 p.Ser624= (c.1872C>T) is rare (popmax 0.216%, afr) (gnomAD).

TRAF7 p.Ser624=

c.1872C>T · rs142534945 · VCV3054586

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.216%, afr)

Conditions

TRAF7-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.47	GERP -2.7, phastCons 0.05
Overall
CADD	7.121	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.216% African / African-American · 162/75,030 alleles

Filtering AF 0.189% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.178%

Overall 0.0114% 183/1,606,052 alleles · rare exomes 99/1,453,726 · genomes 84/152,326 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.216%	463
Admixed American	0.02%	4,993
Remaining individualsnot grpmax-eligible	0.0128%	7,797
European (non-Finnish)	8.48e-05%	1,178,953

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: TRAF7
Protein: p.Ser624=
Coding: c.1872C>T
MANE Select: NM_032271
dbSNP: rs142534945
Type: single nucleotide variant
Location: chr16:2176174 (GRCh38)
Gene constraint: LOEUF 0.675 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 80.16 · 1 PDB

Full TRAF7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

TRAF7-related disorder

Similar variants

TRAF7 p.Arg524Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
TRAF7 p.Arg655Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
TRAF7 p.Leu625Phe Likely pathogenic ★ same condition
TRAF7 p.Phe617Ser Likely pathogenic ★ same condition
TRAF7 p.Ser663Thr Likely pathogenic ★ ⚠ same condition
TRAF7 c.1346+3G>A Uncertain significance ★ same condition
TRAF7 p.Arg547Ter Uncertain significance ★ same condition
TRAF7 p.His299Gln 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/traf7-p-ser624 (accessed [today's date]).

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